An evolutionarily structured universe of protein architecture

被引:134
作者
Caetano-Anollés, G
Caetano-Anollés, D
机构
[1] Vital NRG, Knoxville, TN 37919 USA
[2] Univ Illinois, Dept Crop Sci, Urbana, IL 61801 USA
关键词
D O I
10.1101/gr.1161903
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Protein structural diversity encompasses a finite set of architectural designs. Embedded in these topologies are evolutionary histories that we here uncover using cladistic principles and measurements of protein-fold usage and sharing. The reconstructed phylogenies are inherently rooted and depict histories of protein and proteome diversification. Proteome phylogenies showed two monophyletic sister-groups delimiting Bacteria and Archaea, and a topology rooted in Eucarya. This suggests three dramatic evolutionary events and a common ancestor with a eukaryotic-like, gene-rich, and relatively modern organization. Conversely, a general phylogeny of protein architectures showed that structural classes of globular proteins appeared early in evolution and in defined order, the alpha/beta class being the first. Although most ancestral folds shared a common architecture of barrels or interleaved beta-sheets and alpha-helices, many were clearly derived, such as polyhedral folds in the all-alpha class and beta-sandwiches, beta-propellers, and beta-prisms in all-beta proteins. We also describe transformation pathways of architectures that are prevalently used in nature. For example, beta-barrels with increased curl and stagger were favored evolutionary outcomes in the all-beta class. Interestingly, we found cases where structural change followed the alpha-to-beta tendency uncovered in the tree of architectures. Lastly, we traced the total number of enzymatic functions associated with folds in the trees and show that there is a general link between structure and enzymatic function.
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页码:1563 / 1571
页数:9
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